FEMS microbiology ecology最新文献_第6页

Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members. 从基因组学角度了解嗜酸性耐卤酸杆菌属成员碳、氮和磷酸盐同化的关键机制。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae145

Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin

{"title":"Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.","authors":"Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin","doi":"10.1093/femsec/fiae145","DOIUrl":"10.1093/femsec/fiae145","url":null,"abstract":"In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface. 沉积物-水界面及以下铁质条件下的绿藻群的分类和功能分区。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae140

Aurèle Vuillemin, Fatima Ruiz-Blas, Sizhong Yang, Alexander Bartholomäus, Cynthia Henny, Jens Kallmeyer

{"title":"Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.","authors":"Aurèle Vuillemin, Fatima Ruiz-Blas, Sizhong Yang, Alexander Bartholomäus, Cynthia Henny, Jens Kallmeyer","doi":"10.1093/femsec/fiae140","DOIUrl":"10.1093/femsec/fiae140","url":null,"abstract":"The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum. 荚膜酸杆菌在纳米缺氧条件下的呼吸发酵生存策略

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae152

Daniela Trojan, Emilio García-Robledo, Bela Hausmann, Niels Peter Revsbech, Dagmar Woebken, Stephanie A Eichorst

{"title":"A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.","authors":"Daniela Trojan, Emilio García-Robledo, Bela Hausmann, Niels Peter Revsbech, Dagmar Woebken, Stephanie A Eichorst","doi":"10.1093/femsec/fiae152","DOIUrl":"10.1093/femsec/fiae152","url":null,"abstract":"Microbial soil habitats are characterized by rapid shifts in substrate and nutrient availabilities, as well as chemical and physical parameters. One such parameter that can vary in soil is oxygen; thus, microbial survival is dependent on adaptation to this substrate. To better understand the metabolic abilities and adaptive strategies to oxygen-deprived environments, we combined genomics with transcriptomics of a model organism, Acidobacterium capsulatum, to explore the effect of decreasing, environmentally relevant oxygen concentrations. The decrease from 10 to 0.1 µM oxygen (3.6 to 0.036 pO2% present atmospheric level, respectively) caused the upregulation of the transcription of genes involved in signal transduction mechanisms, energy production and conversion and secondary metabolites biosynthesis, transport, and catabolism based on clusters of orthologous group categories. Contrary to established observations for aerobic metabolism, key genes in oxidative stress response were significantly upregulated at lower oxygen concentrations, presumably due to an NADH/NAD+ redox ratio imbalance as the cells transitioned into nanoxia. Furthermore, A. capsulatum adapted to nanoxia by inducing a respiro-fermentative metabolism and rerouting fluxes of its central carbon and energy pathways to adapt to high NADH/NAD+ redox ratios. Our results reveal physiological features and metabolic capabilities that allowed A. capsulatum to adapt to oxygen-limited conditions, which could expand into other environmentally relevant soil strains.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MetaCompare 2.0: differential ranking of ecological and human health resistome risks. MetaCompare 2.0：生态和人类健康抗蚀体风险的差异排序。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae155

Monjura Afrin Rumi, Min Oh, Benjamin C Davis, Connor L Brown, Adheesh Juvekar, Peter J Vikesland, Amy Pruden, Liqing Zhang

{"title":"MetaCompare 2.0: differential ranking of ecological and human health resistome risks.","authors":"Monjura Afrin Rumi, Min Oh, Benjamin C Davis, Connor L Brown, Adheesh Juvekar, Peter J Vikesland, Amy Pruden, Liqing Zhang","doi":"10.1093/femsec/fiae155","DOIUrl":"10.1093/femsec/fiae155","url":null,"abstract":"While numerous environmental factors contribute to the spread of antibiotic resistance genes (ARGs), quantifying their relative contributions remains a fundamental challenge. Similarly, it is important to differentiate acute human health risks from environmental exposure, versus broader ecological risk of ARG evolution and spread across microbial taxa. Recent studies have proposed various methods for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon original MetaCompare pipeline by differentiating indicators of human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition). The updated pipeline's sensitivity was demonstrated by analyzing diverse publicly-available metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities. MetaCompare 2.0 provided distinct rankings of the metagenomes according to both human health resistome risk and ecological resistome risk, with both scores trending higher when influenced by anthropogenic impact or other stress. We evaluated the robustness of the pipeline to sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias. The risk scores were remarkably consistent despite variations in these technological aspects. We packaged the improved pipeline into a publicly-available web service (http://metacompare.cs.vt.edu/) that provides an easy-to-use interface for computing resistome risk scores and visualizing results.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities. 功能冗余可缓冲多极端环境条件对南部非洲干旱地区土壤微生物群落的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae157

Tomás Sauma-Sánchez, Jaime Alcorta, Javier Tamayo-Leiva, Beatriz Díez, Hugo Bezuidenhout, Don A Cowan, Jean-Baptiste Ramond

{"title":"Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.","authors":"Tomás Sauma-Sánchez, Jaime Alcorta, Javier Tamayo-Leiva, Beatriz Díez, Hugo Bezuidenhout, Don A Cowan, Jean-Baptiste Ramond","doi":"10.1093/femsec/fiae157","DOIUrl":"10.1093/femsec/fiae157","url":null,"abstract":"Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11636270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss. 弗兰科菌[NiFe]摄取氢化酶和基因组减少：损失的不同系列。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae147

Katharina Pawlowski, Daniel Wibberg, Sara Mehrabi, Nadia Binte Obaid, András Patyi, Fede Berckx, Han Nguyen, Michelle Hagen, Daniel Lundin, Andreas Brachmann, Jochen Blom, Aude Herrera-Belaroussi, Danis Abrouk, Petar Pujic, Ann-Sofi Hahlin, Jörn Kalinowski, Philippe Normand, Anita Sellstedt

{"title":"Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss.","authors":"Katharina Pawlowski, Daniel Wibberg, Sara Mehrabi, Nadia Binte Obaid, András Patyi, Fede Berckx, Han Nguyen, Michelle Hagen, Daniel Lundin, Andreas Brachmann, Jochen Blom, Aude Herrera-Belaroussi, Danis Abrouk, Petar Pujic, Ann-Sofi Hahlin, Jörn Kalinowski, Philippe Normand, Anita Sellstedt","doi":"10.1093/femsec/fiae147","DOIUrl":"10.1093/femsec/fiae147","url":null,"abstract":"Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup-, while only one Hup- Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emergence of dauer larvae in Caenorhabditis elegans disrupts continuity of host-microbiome interactions. 秀丽隐杆线虫(Caenorhabditis elegans)中出现的畸形幼虫破坏了宿主与微生物组相互作用的连续性。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae149

Rahul Bodkhe, Kenneth Trang, Sabrina Hammond, Da Kyung Jung, Michael Shapira

{"title":"Emergence of dauer larvae in Caenorhabditis elegans disrupts continuity of host-microbiome interactions.","authors":"Rahul Bodkhe, Kenneth Trang, Sabrina Hammond, Da Kyung Jung, Michael Shapira","doi":"10.1093/femsec/fiae149","DOIUrl":"10.1093/femsec/fiae149","url":null,"abstract":"Nematodes are common in most terrestrial environments, where populations are often known to undergo cycles of boom and bust. Useful in such scenarios, nematodes present developmental programs of diapause, giving rise to stress-resistant larvae and enabling dispersal in search of new resources. Best studied in Caenorhabditis elegans, stress resistant dauer larvae emerge under adverse conditions, primarily starvation, and migrate to new niches where they can resume development and reproduce. Caenorhabditis elegans is a bacterivore but has been shown to harbor a persistent and characteristic gut microbiome. While much is known about the gut microbiome of reproducing C. elegans, what dauers harbor is yet unknown. This is of interest, as dauers are those that would enable transmission of microbes between nematode generations and geographical sites, maintaining continuity of host-microbe interactions. Using culture-dependent as well as sequencing-based approaches, we examined the gut microbiomes of dauers emerging following population growth on ten different natural-like microbially diverse environments as well as on two defined communities of known gut commensals and found that dauers were largely devoid of gut bacteria. These results suggest that host gut-microbiome interactions in C. elegans are not continuous across successive generations and may reduce the likelihood of long-term worm-microbe coevolution.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean. 纬度梯度和海洋锋面对南太平洋地区的原生生物群落有很大影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae137

Daniela Sturm, Peter Morton, Gerald Langer, William M Balch, Glen Wheeler

{"title":"Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean.","authors":"Daniela Sturm, Peter Morton, Gerald Langer, William M Balch, Glen Wheeler","doi":"10.1093/femsec/fiae137","DOIUrl":"10.1093/femsec/fiae137","url":null,"abstract":"Protist communities in the southern Pacific Ocean make a major contribution to global biogeochemical cycling, but remain understudied due to their remote location. We therefore have limited understanding of how large-scale physical gradients (e.g. temperature) and mesoscale oceanographic features (e.g. fronts) influence microeukaryote diversity in this region. We performed a high-resolution examination of protist communities along a latitudinal transect (>3000 km) at 150°W in the central southern Pacific Ocean that encompassed major frontal regions, including the subtropical front (STF), the subantarctic front (SAF), and the polar front (PF). We identified distinct microbial communities along the transect that were primarily delineated by the positions of the STF and PF. Some taxa were not constricted by these environmental boundaries and were able to span frontal regions, such as the colonial haptophyte Phaeocystis. Our findings also support the presence of a latitudinal diversity gradient (LDG) of decreasing diversity of the protist community with increasing latitude, although some individual taxa, notably the diatoms, do not adhere to this rule. Our findings show that oceanographic features and large-scale physical gradients have important impacts on marine protist communities in the southern Pacific Ocean that are likely to strongly influence their response to future environmental change.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11653569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ecological processes shaping highly connected bacterial communities along strong environmental gradients. 沿着强烈的环境梯度塑造高度关联细菌群落的生态过程。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae146

Wenxue Wu, Chih-Hao Hsieh, Ramiro Logares, Jay T Lennon, Hongbin Liu

{"title":"Ecological processes shaping highly connected bacterial communities along strong environmental gradients.","authors":"Wenxue Wu, Chih-Hao Hsieh, Ramiro Logares, Jay T Lennon, Hongbin Liu","doi":"10.1093/femsec/fiae146","DOIUrl":"10.1093/femsec/fiae146","url":null,"abstract":"Along the river-sea continuum, microorganisms are directionally dispersed by water flow while being exposed to strong environmental gradients. To compare the two assembly mechanisms that may strongly and differently influence metacommunity dynamics, namely homogenizing dispersal and heterogeneous selection, we characterized the total (16S rRNA gene) and putatively active (16S rRNA transcript) bacterial communities in the Pearl River-South China Sea Continuum, during the wet (summer) and dry (winter) seasons using high-throughput sequencing. Moreover, well-defined sampling was conducted by including freshwater, oligohaline, mesohaline, polyhaline, and marine habitats. We found that heterogeneous selection exceeded homogenizing dispersal in both the total and active fractions of bacterial communities in two seasons. However, homogeneous selection was prevalent (the dominant except in active bacterial communities during summer), which was primarily due to the bacterial communities' tremendous diversity (associated with high rarity) and our specific sampling design. In either summer or winter seasons, homogeneous and heterogeneous selection showed higher relative importance in total and active communities, respectively, implying that the active bacteria were more responsive to environmental gradients than were the total bacteria. In summary, our findings provide insight into the assembly of bacterial communities in natural ecosystems with high spatial connectivity and environmental heterogeneity.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142544588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Seasonal shifts and land-use impact: unveiling the gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis). 季节变化和土地利用影响：揭示银行田鼠（Myodes glareolus）和普通田鼠（Microtus arvalis）的肠道微生物组。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-11-23 DOI: 10.1093/femsec/fiae159

Lea Kauer, Christian Imholt, Jens Jacob, Christian Berens, Ralph Kühn

{"title":"Seasonal shifts and land-use impact: unveiling the gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis).","authors":"Lea Kauer, Christian Imholt, Jens Jacob, Christian Berens, Ralph Kühn","doi":"10.1093/femsec/fiae159","DOIUrl":"10.1093/femsec/fiae159","url":null,"abstract":"Gut microbial diversity influences the health and vitality of the host, yet it is itself affected by internal and external factors, including land-use. The impact of land-use practices on wild rodents' gut microbiomes remains understudied, despite their abundance and potential as reservoirs for zoonotic pathogens. We examined the bacterial and fungal gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis) across grassland and forest habitats with varying land-use intensities and types. We collected rodents seasonally and used 16S rRNA and ITS amplicon sequencing for microbe identification. We found significant differences in alpha and beta diversities between the species, with M. arvalis exhibiting higher diversity. Seasonality emerged as a prominent factor influencing microbial diversity, with significant variations between sampling months. While land-use affects the gut microbiome, its impact is subordinate to seasonal variations. Differential abundance analysis underscores the dynamic nature of microbial composition, with seasonal changes playing a predominant role. Overall, our findings highlight the significant influence of seasonality on gut microbiome diversity and composition in wild rodents, reflecting dietary shifts associated with seasonal changes. Understanding the interplay between environmental factors and microbial communities in wild rodents enahnces our knowledge of ecosystem health and resilience, warranting further investigation.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11650868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0